Contacts of the strand formed by residues 23 - 25 (chain M) in PDB entry 7K60


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with MET 23 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21M  ILE*     3.5    10.9    +      -       -      +
     22M  LYS*     1.3    83.0    +      -       -      +
     24M  THR*     1.3    59.5    +      -       -      +
     25M  GLN      3.7     1.8    +      -       -      -
     42M  CYS*     3.3    28.0    -      -       -      -
     43M  LYS      3.8     0.7    -      -       -      -
     44M  ALA*     3.6    34.8    -      -       +      +
     48M  ILE*     4.5     0.7    -      -       -      -
     52M  LEU*     3.6    25.6    -      -       +      -
     90M  PHE*     5.1     0.2    -      -       +      -
    107M  CYS*     3.6    16.8    -      -       -      -
    109M  GLN*     3.5    36.8    -      -       +      -
    116M  THR*     4.0    12.0    -      -       +      +
    117M  PHE      4.1    10.5    -      -       -      +
    118M  GLY*     3.6    15.9    -      -       -      -
    119M  SER*     4.0     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 24 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22M  LYS*     4.0    14.7    +      -       -      +
     23M  MET*     1.3    70.6    -      -       -      +
     25M  GLN*     1.3    66.0    +      -       -      +
     26M  SER*     3.3     7.5    +      -       -      +
     42M  CYS*     3.4     4.1    -      -       -      -
     43M  LYS*     2.7    52.0    +      -       +      +
     45M  SER*     5.6     0.3    +      -       -      -
    119M  SER*     5.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 25 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23M  MET      3.7     3.0    +      -       -      -
     24M  THR*     1.3    74.9    -      -       -      +
     26M  SER*     1.3    65.9    +      -       -      +
     27M  PRO*     3.7     0.7    -      -       +      -
     28M  SER*     4.1     8.1    +      -       -      -
     40M  ILE*     3.8     4.0    -      -       -      +
     41M  THR      3.6     7.0    -      -       -      +
     42M  CYS*     3.5    23.8    -      -       +      -
     54M  TRP*     3.7    16.5    -      -       -      -
    105M  TYR      3.0    24.9    +      -       -      +
    106M  TYR*     3.4     1.6    -      -       -      -
    107M  CYS*     3.3    23.1    +      -       -      -
    118M  GLY*     3.7     6.5    -      -       -      -
    119M  SER*     3.9    20.8    +      -       -      +
    120M  GLY      3.1    22.9    +      -       -      +
    121M  THR*     3.0    27.7    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il